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Aliases for CLRN1 Gene

Aliases for CLRN1 Gene

  • Clarin 1 2 3
  • USH3A 3 4 6
  • Usher Syndrome Type-3 Protein 3 4
  • RP61 3 6
  • USH3 3 6
  • Usher Syndrome 3A 2
  • Clarin-1 3

External Ids for CLRN1 Gene

Previous HGNC Symbols for CLRN1 Gene

  • USH3
  • USH3A
  • RP61

Previous GeneCards Identifiers for CLRN1 Gene

  • GC03M152127
  • GC03M150643
  • GC03M148017

Summaries for CLRN1 Gene

Entrez Gene Summary for CLRN1 Gene

  • This gene encodes a protein that contains a cytosolic N-terminus, multiple helical transmembrane domains, and an endoplasmic reticulum membrane retention signal, TKGH, in the C-terminus. The encoded protein may be important in development and homeostasis of the inner ear and retina. Mutations within this gene have been associated with Usher syndrome type IIIa. Multiple transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for CLRN1 Gene

CLRN1 (Clarin 1) is a Protein Coding gene. Diseases associated with CLRN1 include retinitis pigmentosa 61 and usher syndrome, type 3a. An important paralog of this gene is CLRN3.

UniProtKB/Swiss-Prot for CLRN1 Gene

  • May have a role in the excitatory ribbon synapse junctions between hair cells and cochlear ganglion cells and presumably also in analogous synapses within the retina.

Gene Wiki entry for CLRN1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLRN1 Gene

Genomics for CLRN1 Gene

Regulatory Elements for CLRN1 Gene

Genomic Location for CLRN1 Gene

150,926,163 bp from pter
150,972,999 bp from pter
46,837 bases
Minus strand

Genomic View for CLRN1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for CLRN1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLRN1 Gene

Proteins for CLRN1 Gene

  • Protein details for CLRN1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • D3DNJ3
    • E1ACU9
    • Q8N6A9

    Protein attributes for CLRN1 Gene

    232 amino acids
    Molecular mass:
    25719 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for CLRN1 Gene


neXtProt entry for CLRN1 Gene

Proteomics data for CLRN1 Gene at MOPED

Post-translational modifications for CLRN1 Gene

  • Glycosylation at Asn48
  • Modification sites at PhosphoSitePlus

Other Protein References for CLRN1 Gene

Antibody Products

No data available for DME Specific Peptides for CLRN1 Gene

Domains for CLRN1 Gene

Protein Domains for CLRN1 Gene


Suggested Antigen Peptide Sequences for CLRN1 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the clarin family.
  • Belongs to the clarin family.
genes like me logo Genes that share domains with CLRN1: view

No data available for Gene Families for CLRN1 Gene

Function for CLRN1 Gene

Molecular function for CLRN1 Gene

UniProtKB/Swiss-Prot Function:
May have a role in the excitatory ribbon synapse junctions between hair cells and cochlear ganglion cells and presumably also in analogous synapses within the retina.
genes like me logo Genes that share phenotypes with CLRN1: view

Animal Models for CLRN1 Gene

MGI Knock Outs for CLRN1:

Animal Model Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , miRNA , Transcription Factor Targets and HOMER Transcription for CLRN1 Gene

Localization for CLRN1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLRN1 Gene

Membrane; Multi-pass membrane protein.

Subcellular locations from

Jensen Localization Image for CLRN1 Gene COMPARTMENTS Subcellular localization image for CLRN1 gene
Compartment Confidence
plasma membrane 5
extracellular 1

Gene Ontology (GO) - Cellular Components for CLRN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IDA 19423712
GO:0005902 microvillus IDA 19423712
GO:0016021 integral component of membrane IEA --
GO:0030027 lamellipodium IDA 19423712
genes like me logo Genes that share ontologies with CLRN1: view

Pathways for CLRN1 Gene

SuperPathways for CLRN1 Gene

No Data Available

Interacting Proteins for CLRN1 Gene

Gene Ontology (GO) - Biological Process for CLRN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007015 actin filament organization IDA 19423712
GO:0007601 visual perception IEA --
GO:0007605 sensory perception of sound IMP 15650299
GO:0010592 positive regulation of lamellipodium assembly IDA 19423712
GO:0045494 photoreceptor cell maintenance IMP 15521980
genes like me logo Genes that share ontologies with CLRN1: view

No data available for Pathways by source for CLRN1 Gene

Transcripts for CLRN1 Gene

Unigene Clusters for CLRN1 Gene

Clarin 1:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for CLRN1 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3 ^ 4a · 4b · 4c ^ 5a · 5b ^ 6
SP1: - - -
SP2: - - - -
SP4: - -
SP5: - - -

Relevant External Links for CLRN1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CLRN1 Gene

mRNA expression in normal human tissues for CLRN1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CLRN1 Gene

This gene is overexpressed in Adrenal Gland (37.6).

SOURCE GeneReport for Unigene cluster for CLRN1 Gene Hs.745448

mRNA Expression by UniProt/SwissProt for CLRN1 Gene

Tissue specificity: Widely expressed. Found in the retina
genes like me logo Genes that share expressions with CLRN1: view

Primer Products

In Situ Assay Products

No data available for Protein differential expression in normal tissues , Protein expression and Expression partners for CLRN1 Gene

Orthologs for CLRN1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CLRN1 Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia CLRN1 35
  • 90.23 (n)
  • 93.1 (a)
(Canis familiaris)
Mammalia CLRN1 35
  • 88.51 (n)
  • 92.24 (a)
(Mus musculus)
Mammalia Clrn1 35
  • 85.92 (n)
  • 88.79 (a)
Clrn1 16
(Pan troglodytes)
Mammalia CLRN1 35
  • 98.78 (n)
  • 98.78 (a)
CLRN1 36
  • 99 (a)
(Rattus norvegicus)
Mammalia Clrn1 35
  • 86.21 (n)
  • 90.09 (a)
(Monodelphis domestica)
Mammalia -- 36
  • 84 (a)
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 78 (a)
(Gallus gallus)
Aves CLRN1 35
  • 70.34 (n)
  • 69.8 (a)
-- 36
  • 71 (a)
(Anolis carolinensis)
Reptilia -- 36
  • 72 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia clrn1 35
  • 70.83 (n)
  • 68.1 (a)
(Danio rerio)
Actinopterygii clrn1 35
  • 63.79 (n)
  • 60.78 (a)
clrn1 36
  • 58 (a)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.4175 35
Species with no ortholog for CLRN1:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for CLRN1 Gene

Gene Tree for CLRN1 (if available)
Gene Tree for CLRN1 (if available)

Paralogs for CLRN1 Gene

Paralogs for CLRN1 Gene

(1) SIMAP similar genes for CLRN1 Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with CLRN1: view

Variants for CLRN1 Gene

Sequence variations from dbSNP and Humsavar for CLRN1 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type MAF
rs590596 -- 150,960,857(-) GACTG(C/T)GTGGG intron-variant
rs688776 -- 150,956,172(-) AAAAA(G/T)GTGTG intron-variant
rs744669 -- 150,961,385(+) CAGTA(A/G)TTTTA intron-variant
rs744670 -- 150,961,391(+) TTTTA(A/G)GGACT intron-variant
rs768196 -- 150,928,575(-) TCATA(C/G/T)CAGTG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for CLRN1 Gene

Variant ID Type Subtype PubMed ID
esv275573 CNV Gain+Loss 21479260

Relevant External Links for CLRN1 Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)
Locus Specific Mutation Databases (LSDB)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLRN1 Gene

Disorders for CLRN1 Gene

(2) OMIM Diseases for CLRN1 Gene (606397)


  • Usher syndrome 3A (USH3A) [MIM:276902]: USH is a genetically heterogeneous condition characterized by the association of retinitis pigmentosa with sensorineural deafness. Age at onset and differences in auditory and vestibular function distinguish Usher syndrome type 1 (USH1), Usher syndrome type 2 (USH2) and Usher syndrome type 3 (USH3). USH3 is characterized by postlingual, progressive hearing loss, variable vestibular dysfunction, and onset of retinitis pigmentosa symptoms, including nyctalopia, constriction of the visual fields, and loss of central visual acuity, usually by the second decade of life. {ECO:0000269 PubMed:11524702, ECO:0000269 PubMed:12080385, ECO:0000269 PubMed:12145752, ECO:0000269 PubMed:15521980, ECO:0000269 PubMed:18273898, ECO:0000269 PubMed:23304067}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Retinitis pigmentosa 61 (RP61) [MIM:614180]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. {ECO:0000269 PubMed:21310491}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(2) University of Copenhagen DISEASES for CLRN1 Gene

(1) Novoseek inferred disease relationships for CLRN1 Gene

Disease -log(P) Hits PubMed IDs
usher syndrome 94.4 6

Relevant External Links for CLRN1

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
genes like me logo Genes that share disorders with CLRN1: view

No data available for Genatlas for CLRN1 Gene

Publications for CLRN1 Gene

  1. Usher syndrome type III: revised genomic structure of the USH3 gene and identification of novel mutations. (PMID: 12145752) Fields R.R. … Sumegi J. (Am. J. Hum. Genet. 2002) 3 4 23
  2. Mutation screening of USH3 gene (clarin-1) in Spanish patients with Usher syndrome: low prevalence and phenotypic variability. (PMID: 15521980) Aller E. … Millan J.M. (Clin. Genet. 2004) 3 4 23
  3. Disease-causing mutations in the CLRN1 gene alter normal CLRN1 protein trafficking to the plasma membrane. (PMID: 19753315) Isosomppi J. … Sankila E.M. (Mol. Vis. 2009) 3 23
  4. Assignment of an Usher syndrome type III (USH3) gene to chromosome 3q. (PMID: 7711740) Sankila E.M. … de la Chapelle A. (Hum. Mol. Genet. 1995) 2 3
  5. Mutations in a novel gene with transmembrane domains underlie Usher syndrome type 3. (PMID: 11524702) Joensuu T. … Sankila E.-M. (Am. J. Hum. Genet. 2001) 3 4

Products for CLRN1 Gene

Sources for CLRN1 Gene

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